Discussion group for the ARIA software

["Rafid Feisal" <rafidfei AT ualberta.ca>]

Hi,
It seems as though I cannot convert the NMRView Peak file for my CNOESY
spectrum into ARIA XML format on ARIA Web. It converts the N-NOESY spectrum
easily as well the ppm.out file. However, it stops at converting CNOESY
spectrum. Here's the error that I get:

stdout:

ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.

If you use this software, please quote the following reference(s):

Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382


Starting data conversion ...

MESSAGE [SequenceList]: reading sequence /pasteur/zeus/projets/p00/galaxy-
prod/
                        galaxy-dist/database/job_working_directory/004/515/
                        4515416/working/arlrdbp.seq
                        reading /pasteur/zeus/projets/p00/galaxy-prod/
                        galaxy-dist/database/job_working_directory/004/515/
                        4515416/working/arlrdbp.seq
MESSAGE [Converter]: Sequence file(s) "/pasteur/zeus/projets/p00/galaxy-prod/
                     galaxy-dist/database/job_working_directory/
004/515/4515416/
                     working/arlrdbp.seq" read, converted to XML and written
to
                     "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/
                     database/job_working_directory/004/515/4515416/working/
xml/
                     molecule_1873.xml".
MESSAGE [PpmList]: reading a NMRView .out file /pasteur/zeus/projets/p00/
                   galaxy-prod/galaxy-dist/database/job_working_directory/004/
                   515/4515416/working/ppm_Run14.out
                   reading /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/
                   database/job_working_directory/004/515/4515416/working/
                   ppm_Run14.out
MESSAGE [Converter]: Chemical-shift file "/pasteur/zeus/projets/p00/galaxy-
prod/
                     galaxy-dist/database/job_working_directory/
004/515/4515416/
                     working/ppm_Run14.out" read, converted to XML and written
                     to "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/
                     database/job_working_directory/004/515/4515416/working/
xml/
                     chemicalshift_3551_ppm_Run14_1873.xml".
MESSAGE [NoeList]: NMRView file /pasteur/zeus/projets/p00/galaxy-prod/
                   galaxy-dist/database/job_working_directory/004/515/4515416/
                   working/hcnoesy_Run14.xpk contains 3 dimensions: ['HC',
'H',
                   'C']


stderr:
Traceback (most recent call last):
  File "/opt/aria2.3/aria2.py", line 912, in
    convert_data(args)
  File "/opt/aria2.3/aria2.py", line 636, in convert_data
    converter.convert(filename)
  File "/opt/aria2.3/src/py/aria/conversion.py", line 2637, in convert
    [self._convert_spectrum(i) for i in range(len(settings['spectrum']))]
  File "/opt/aria2.3/src/py/aria/conversion.py", line 2428, in
_convert_spectrum
    self._convert_crosspeaks(number)
  File "/opt/aria2.3/src/py/aria/conversion.py", line 2396, in
_convert_crosspeaks
    naming_convention, segids, settings['spectrum_ambiguity']) ## BARDIAUX 2.2
  File "/opt/aria2.3/src/py/aria/conversion.py", line 1805, in create_spectrum
    if c.residue1 is not None: base1 = chain[s].get(int(c.residue1))
ValueError: invalid literal for int() with base 10: 'Y77'

/usr/share/misc/magic, 21623: Warning: `name    pgpkey' entries can only be
declared at top level
/usr/share/misc/magic, 27403: Warning: using regular magic file `/usr/share/
misc/bioinfo'
/usr/share/misc/magic, 21623: Warning: `name    pgpkey' entries can only be
declared at top level
/usr/share/misc/magic, 27403: Warning: using regular magic file `/usr/share/
misc/bioinfo'

I managed to convert files easily before. Also for the naming convention for
sequence, I selected IUPAC. Any advice would be highly appreciated.

Thank you.
Regards,
Rafid